title: Discovering regulatory overlapping RNA transcripts.
abstract: STEREO is a novel algorithm that discovers cis-regulatory RNA interactions by assembling complete and potentially overlapping same-strand RNA transcripts from tiling expression data. STEREO first identifies coherent segments of transcription and then discovers individual transcripts that are consistent with the observed segments given intensity and shape constraints. We used STEREO to identify 1446 regions of overlapping transcription in two strains of yeast, including transcripts that comprise a new form of molecular toggle switch that controls gene variegation.
authors.affiliation: Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. tdanford@gmail.com
authors.forename: Timothy
authors.initials: T
authors.lastname: Danford
authors.forename: Robin
authors.initials: R
authors.lastname: Dowell
authors.forename: Sudeep
authors.initials: S
authors.lastname: Agarwala
authors.forename: Paula
authors.initials: P
authors.lastname: Grisafi
authors.forename: Gerald
authors.initials: G
authors.lastname: Fink
authors.forename: David
authors.initials: D
authors.lastname: Gifford
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D015966:Gene Expression Regulation, Fungal; D023281:Genomics / Q000379:methods*; D008957:Models, Genetic; D050543:Phosphoglycerate Dehydrogenase / Q000235:genetics; D011401:Promoter Regions, Genetic; D012331:RNA, Fungal / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics; D014158:Transcription, Genetic
chemical_list: D012331:RNA, Fungal; D029701:Saccharomyces cerevisiae Proteins; D050543:Phosphoglycerate Dehydrogenase; C493278:SER3 protein, S cerevisiae